Julio Saez-Rodriguez
Orcid: 0000-0002-8552-8976
According to our database1,
Julio Saez-Rodriguez
authored at least 69 papers
between 2001 and 2024.
Collaborative distances:
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Bibliography
2024
2023
CoRR, 2023
2022
Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.
PLoS Comput. Biol., 2022
Expert Syst. Appl., 2022
CoRR, 2022
Bioinform., 2022
2021
A comprehensive database for integrated analysis of omics data in autoimmune diseases.
BMC Bioinform., 2021
Bioinform., 2021
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.
Bioinform., 2021
Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Briefings Bioinform., 2021
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling.
Briefings Bioinform., 2021
2020
Medical Image Anal., 2020
Converting networks to predictive logic models from perturbation signalling data with CellNOpt.
Bioinform., 2020
Bioinform., 2020
2019
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology.
J. Supercomput., 2019
Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders.
CoRR, 2019
2018
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data.
PLoS Comput. Biol., 2018
A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
PLoS Comput. Biol., 2018
PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks.
CoRR, 2018
2017
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
PLoS Comput. Biol., 2017
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
PLoS Comput. Biol., 2017
caspo: a toolbox for automated reasoning on the response of logical signaling networks families.
Bioinform., 2017
Bioinform., 2017
2016
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinform., 2016
Efficient randomization of biological networks while preserving functional characterization of individual nodes.
BMC Bioinform., 2016
2015
Theor. Comput. Sci., 2015
F1000Research, 2015
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
BMC Syst. Biol., 2015
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
BMC Bioinform., 2015
Bioinform., 2015
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Bioinform., 2015
2014
CoRR, 2014
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol., 2014
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC Bioinform., 2014
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Biosyst., 2014
Bioinform., 2014
2013
<i>Cyrface</i>: An interface from <i>Cytoscape</i> to <i>R </i>that provides a user interface to <i>R</i> packages.
F1000Research, 2013
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
CoRR, 2013
BMC Syst. Biol., 2013
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013
Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Bioinform., 2013
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Bioinform., 2013
BioServices: a common Python package to access biological Web Services programmatically.
Bioinform., 2013
2012
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
CoRR, 2012
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming
CoRR, 2012
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
BMC Syst. Biol., 2012
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
BMC Syst. Biol., 2012
Bioinform., 2012
Proceedings of the Computational Methods in Systems Biology, 2012
2011
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli.
PLoS Comput. Biol., 2011
2009
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
PLoS Comput. Biol., 2009
Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data.
PLoS Comput. Biol., 2009
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling.
PLoS Comput. Biol., 2009
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
BMC Syst. Biol., 2009
2008
Flexible informatics for linking experimental data to mathematical models via <i>DataRail</i>.
Bioinform., 2008
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
Proceedings of the ECCB'08 Proceedings, 2008
2007
PLoS Comput. Biol., 2007
BMC Syst. Biol., 2007
2006
BMC Bioinform., 2006
A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC Bioinform., 2006
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
BMC Bioinform., 2006
2005
Comput. Chem. Eng., 2005
2001
Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001